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The development of high quality, non-toxic ( i.e. , heavy-metal-free), and functional quantum dots (QDs) via ‘green’ and scalable synthesis routes is critical for realizing truly sustainable QD-based solutions to diverse technological challenges. Herein, we demonstrate the low-temperature all-aqueous-phase synthesis of silver indium sulfide/zinc (AIS/Zn) QDs with a process initiated by the biomineralization of highly crystalline indium sulfide nanocrystals, and followed by the sequential staging of Ag + cation exchange and Zn 2+ addition directly within the biomineralization media without any intermediate product purification. Therein, we exploit solution phase cation concentration, the duration of incubation in the presence of In 2 S 3 precursor nanocrystals, and the subsequent addition of Zn 2+ as facile handles under biomineralization conditions for controlling QD composition, tuning optical properties, and improving the photoluminescence quantum yield of the AIS/Zn product. We demonstrate how engineering biomineralization for the synthesis of intrinsically hydrophilic and thus readily functionalizable AIS/Zn QDs with a quantum yield of 18% offers a ‘green’ and non-toxic materials platform for targeted bioimaging in sensitive cellular systems. Ultimately, the decoupling of synthetic steps helps unravel the complexities of ion exchange-based synthesis within the biomineralization platform, enabling its adaptation for the sustainable synthesis of ‘green’, compositionally diverse QDs.